GAMESS-2013May01 for PRIMERGY
Webpage
http://www.msg.ameslab.gov/GAMESS/GAMESS.html

VersionMay 1, 2013

Tools for CompilingIntel Compiler 13.1.1.163
Intel MPI 4.0.2.003

Necessary Files for Compilinggamess-2013May01.tar.gz (from GAMESS webpage)
rungms.patch

Content of rungms.patch--- rungms 2013-08-20 17:19:34.411587000 +0900+++ rungms.new 2013-08-20 17:19:20.322722000 +0900@@ -59,10 +59,10 @@#both Sun Grid Engine (SGE), and Portable Batch System (PBS).
#See also a very old LoadLeveler "ll-gms" for some IBM systems.
#-set TARGET=sockets-set SCR=/scr/$USER-set USERSCR=~$USER/scr-set GMSPATH=/u1/mike/gamess+set TARGET=mpi+set SCR=/work/users/$USER/scr.$$+if (! -d $SCR) mkdir $SCR
+set GMSPATH=/local/apl/pg/gamess2013May01#
set JOB=$1# name of the input file xxx.inp, give only the xxx partset VERNO=$2 # revision number of the executable created by 'lked' step@@ -92,16 +92,10 @@uniq $TMPDIR/machines
endif
if ($SCHED == PBS) then- set SCR=/scratch/$PBS_JOBID+# set SCR=/scratch/$PBS_JOBID
echo "PBS has assigned the following compute nodes to this run:"
uniq $PBS_NODEFILE
endif-#-echo "Available scratch disk space (Kbyte units) at beginning of the job is"-df -k $SCR
-echo "GAMESS temporary binary files will be written to $SCR"-echo "GAMESS supplementary output files will be written to $USERSCR"#
this added as experiment, February 2007#
its intent is to detect large arrays allocated off the stacklimit stacksize 8192@@ -134,6 +128,15 @@endifendif+set dir=`dirname $JOB`+set USERSCR=`cd $dir; pwd`+

+#+echo "Available scratch disk space (Kbyte units) at beginning of the job is"+df -k $SCR
+echo "GAMESS temporary binary files will be written to $SCR"+echo "GAMESS supplementary output files will be written to $USERSCR"+# define many environment variables setting up file names.
# anything can be overridden by a user's own choice, read 2nd.
source $GMSPATH/gms-files.csh@@ -742,7 +745,7 @@setenv I_MPI_DEBUG 0
setenv I_MPI_STATS 0
setenv I_MPI_FABRICS dapl
setenv I_MPI_DAT_LIBRARY libdat2.so+setenv I_MPI_DAT_LIBRARY libdat2.so.2#in case someone wants to try the "tag matching interface",#an option which unfortunately ignores the WAIT_MODE in 4.0.2!
#--setenv I_MPI_FABRICS tmi@@ -1436,6 +1439,7 @@echo Files used on the master node $master were:ls -lF $SCR/$JOB.*
rm -f $SCR/$JOB.F*+rm -f $SCR/$JOB.nodes.mpd## Clean/Rescue any files created by the VB2000 plug-in
if (-e $SCR/$JOB.V84)
mv $SCR/$JOB.V84$USERSCR@@ -1447,13 +1451,13 @@if (-e $SCR/$JOB.molf)
mv $SCR/$JOB.molf $USERSCR
if (-e $SCR/$JOB.mkl)
mv $SCR/$JOB.mkl$USERSCR
if (-e $SCR/$JOB.xyz)
mv $SCR/$JOB.xyz$USERSCR-ls $SCR/${JOB}-*.cube > $SCR/${JOB}.lis+(ls $SCR/${JOB}-*.cube > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.cube $USERSCR
rm -f $SCR/${JOB}.lis-ls $SCR/${JOB}-*.grd > $SCR/${JOB}.lis+(ls $SCR/${JOB}-*.grd > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.grd $USERSCR
rm -f $SCR/${JOB}.lis-ls $SCR/${JOB}-*.csv > $SCR/${JOB}.lis+(ls $SCR/${JOB}-*.csv > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.csv $USERSCR
rm -f $SCR/${JOB}.lis#@@ -1487,37 +1491,37 @@# We have inherited a file of unique node names from above.
# There is an option to rescue the output files from group DDI runs,# such as FMO, in case you need to see the other group's outputs.
-if ($TARGET == mpi) then- set nnodes=`wc -l $HOSTFILE`- set nnodes=$nnodes[1]- @ n=1- set master=`hostname`# burn off the .local suffix in our cluster's hostname- set master=$master:r- while ($n <= $nnodes)
set host=`sed -n -e "$n p" $HOSTFILE`# in case of openMPI, unwanted stuff may follow the hostname
set host=$host[1]if ($host != $master) thenecho Files used on node $host were:#---------FMO rescue-----#--if ($GDDIjob == true) then#-- echo "========= OUTPUT from node $host is =============="#-- ssh $host -l $USER "cat $SCR/$JOB.F06*"#--endif

#---------FMO rescue-----ssh $host -l $USER "ls -l $SCR/$JOB.*"ssh $host -l $USER "rm -f $SCR/$JOB.*"
endif@ n++- end-#clean off the last file on the master's scratch disk.
- rm -f $HOSTFILE- #- if ($?I_MPI_STATS) thenif ($I_MPI_STATS > 0) mv $SCR/stats.txt ~/$JOB.$NCPUS.stats- endif-endif+###if ($TARGET == mpi) then+### set nnodes=`wc -l $HOSTFILE`+### set nnodes=$nnodes[1]+### @ n=1+### set master=`hostname`+#### burn off the .local suffix in our cluster's hostname+### set master=$master:r+### while ($n <= $nnodes)+###
set host=`sed -n -e "$n p" $HOSTFILE`+#### in case of openMPI, unwanted stuff may follow the hostname+###
set host=$host[1]+###if ($host != $master) then+###echo Files used on node $host were:+####---------FMO rescue-----+####--if ($GDDIjob == true) then+####-- echo "========= OUTPUT from node $host is =============="+####-- ssh $host -l $USER "cat $SCR/$JOB.F06*"+####--endif+####---------FMO rescue-----+###
ssh $host -l $USER "ls -l $SCR/$JOB.*"+###ssh $host -l $USER "rm -f $SCR/$JOB.*"+###endif+###@ n+++### end+####
clean off the last file on the master's scratch disk.
+### rm -f $HOSTFILE+### #+### if ($?I_MPI_STATS) then+###if ($I_MPI_STATS > 0) mv $SCR/stats.txt ~/$JOB.$NCPUS.stats+### endif+###endif## IBM SP cleanup code...might need to be something other than 'rsh'.
#Procedure of Compiling#!/bin/csh -f
umask 022
set file_gamess=/home/users/${USER}/build/gamess2013May01/gamess-2013May01.tar.gz
set work=/work/users/${USER}
set gamess=gamess2013May01
set patch_rungms=/home/users/${USER}/build/gamess2013May01/ccpg/rungms.patch#---------------------------------------------------------------------------cd ${work}
if (-d ${gamess}) thenmv ${gamess} ${gamess}-erase
rm -rf ${gamess}-erase &endif#---------------------------------------------------------------------------tar xzf ${file_gamess}
mv gamess ${gamess}
cd ${work}/${gamess}expect <<EXPECT
spawn ./config
expect "After the new window is open"
send "\r"expect "please enter your target machine name:"
send "linux64\r"
expect "GAMESS directory?"
send "\r"expect "GAMESS build directory?"
send "\r"expect "Version?"
send "\r"expect "Please enter your choice of FORTRAN:"
send "ifort\r"
expect "Version?"
send "12\r"
expect "hit <return> to continue after digesting this message."send "\r"expect "hit <return> to continue to the math library setup."
send "\r"expect "Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none':"send "mkl\r"
expect "MKL pathname?"
send "/opt/intel/mkl\r"
expect "MKL version (or 'skip')?"send "skip\r"
expect "hit <return> after you have digested this warning."
send "\r"expect "please hit <return> to compile the GAMESS source code activator"
send "\r"expect "please hit <return> to set up your network for Linux clusters."
send "\r"expect "communication library ('sockets' or 'mpi')?"send "mpi\r"
expect "Enter MPI library (impi, mvapich2, mpt, sockets):"
send "impi\r"
expect "Please enter your impi's location:"
send "/opt/intel/impi/4.0.2.003\r"
expect "Do you want to try LIBCCHEM"
send "no\r"
expect eofEXPECT#---------------------------------------------------------------------------cd ${work}/${gamess}/ddi./compddi >& compddi.log
cd ${work}/${gamess}./compall >& compall.log./lked >& lked.log#---------------------------------------------------------------------------chmod -R o-rwx source object
find . -name "src" | xargs chmod -R o-rwx#---------------------------------------------------------------------------patch -p0 < ${patch_rungms}